6-106700598-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The variant allele was found at a frequency of 0.859 in 152,238 control chromosomes in the GnomAD database, including 56,295 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.86 ( 56295 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.727
Variant links:

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ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.0).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.871 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.859
AC:
130655
AN:
152120
Hom.:
56233
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.867
Gnomad AMI
AF:
0.867
Gnomad AMR
AF:
0.883
Gnomad ASJ
AF:
0.934
Gnomad EAS
AF:
0.744
Gnomad SAS
AF:
0.768
Gnomad FIN
AF:
0.896
Gnomad MID
AF:
0.826
Gnomad NFE
AF:
0.854
Gnomad OTH
AF:
0.855
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.859
AC:
130777
AN:
152238
Hom.:
56295
Cov.:
32
AF XY:
0.859
AC XY:
63932
AN XY:
74426
show subpopulations
Gnomad4 AFR
AF:
0.868
Gnomad4 AMR
AF:
0.884
Gnomad4 ASJ
AF:
0.934
Gnomad4 EAS
AF:
0.745
Gnomad4 SAS
AF:
0.769
Gnomad4 FIN
AF:
0.896
Gnomad4 NFE
AF:
0.854
Gnomad4 OTH
AF:
0.857
Alfa
AF:
0.855
Hom.:
2756
Bravo
AF:
0.861

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.83
DANN
Benign
0.43

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2798360; hg19: chr6-107148473; API